Out-of-the-Box Proteomics Analysis

Proteomics may be the hot buzzword in biology, but proteomics researchers still lack the integrated, "off-the-shelf" tools that have come to characterize genomic research. Now, however, San Jose, Calif.-based Thermo Finnigan offers these scientists an all-in-one package with its recently released ProteomeX™ Workstation, a complete proteomics system. The ProteomeX Workstation is a multidimensional liquid chromatography/mass spectrometry (LC/MS) package that combines three successful Thermo

May 13, 2002
Paul Thacker
Proteomics may be the hot buzzword in biology, but proteomics researchers still lack the integrated, "off-the-shelf" tools that have come to characterize genomic research. Now, however, San Jose, Calif.-based Thermo Finnigan offers these scientists an all-in-one package with its recently released ProteomeX™ Workstation, a complete proteomics system.

The ProteomeX Workstation is a multidimensional liquid chromatography/mass spectrometry (LC/MS) package that combines three successful Thermo Finnigan components: an LCQ™ Deca XP ion trap mass spectrometer, Surveyor® HPLC, and new BioWorks™ 3.0 software, including TurboSEQUEST®. "This is one-stop shopping for proteomics," says Ken Miller, product marketing manager for proteomics.

The ProteomeX's multidimensional LC/MS allows a researcher to analyze proteins in complex samples, such as bacteria, plasma, or a human cell line. After protease digestion, the peptides in the sample are separated by capillary cation exchange followed by high-resolution reversed-phase LC. The mass spectrometer then detects and sequences the separated peptides. Finally, protein databases are queried with the observed sequences to determine the proteins from which the peptides were derived. Researchers can use the ProteomeX system for other proteomics applications, including high-throughput methods using tandem HPLC columns, in which samples can be loaded on the first column while eluting off the second, greatly diminishing analysis cycle times. And, differentially expressed proteins can be quantified using isotope-coded affinity tag (ICAT™) reagents.

Systems similar to the ProteomeX Workstation do exist, but they are homegrown varieties that require user tweaking and optimization, says Miller. In contrast, he says, ProteomeX is the first integrated system available for proteomics work. "What we have done is pulled various components together and optimized them in a package for the customer. We have taken on the burden of design, development, and optimization so that users can concentrate on their research."

Miller says this system can be put to use by anyone looking at the role of proteins in complex biochemical pathways, and he sees greater refinements in the future as his company continues working with its customers. "We know what scientists want—high-performance systems to answer very specific biological questions," he says. "ProteomeX is the first step."

—Paul D. Thacker

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Thermo Finnigan

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